GapMind for catabolism of small carbon sources

 

Protein N515DRAFT_0382 in Dyella japonica UNC79MFTsu3.2

Annotation: N515DRAFT_0382 MFS transporter, sugar porter (SP) family

Length: 472 amino acids

Source: Dyella79 in FitnessBrowser

Candidate for 23 steps in catabolism of small carbon sources

Pathway Step Score Similar to Id. Cov. Bits Other hit Other id. Other bits
D-cellobiose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
D-glucose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
lactose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
D-maltose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
sucrose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
trehalose catabolism MFS-glucose hi The glucose uptake porter, GluP (characterized) 59% 95% 526.9 D-xylose-proton symporter 38% 306.6
D-fructose catabolism glcP med Glucose/fructose:H+ symporter, GlcP (characterized) 56% 97% 488.4 The glucose uptake porter, GluP 59% 526.9
sucrose catabolism glcP med Glucose/fructose:H+ symporter, GlcP (characterized) 56% 97% 488.4 The glucose uptake porter, GluP 59% 526.9
D-xylose catabolism xylT med Glucose/fructose transport protein (characterized, see rationale) 48% 95% 445.7 The glucose uptake porter, GluP 59% 526.9
L-arabinose catabolism araE lo Arabinose-proton symporter; Arabinose transporter (characterized) 35% 94% 281.6 The glucose uptake porter, GluP 59% 526.9
D-galactose catabolism galP lo Arabinose-proton symporter; Arabinose transporter (characterized) 35% 94% 281.6 The glucose uptake porter, GluP 59% 526.9
myo-inositol catabolism iolT lo Major myo-inositol transporter, IolT1, of 456 aas (characterized) 33% 95% 274.6 The glucose uptake porter, GluP 59% 526.9
myo-inositol catabolism HMIT lo inositol transporter 4 (characterized) 34% 59% 192.2 The glucose uptake porter, GluP 59% 526.9
D-fructose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 78% 189.9 The glucose uptake porter, GluP 59% 526.9
D-mannose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 78% 189.9 The glucose uptake porter, GluP 59% 526.9
sucrose catabolism STP6 lo sugar transport protein 6 (characterized) 32% 78% 189.9 The glucose uptake porter, GluP 59% 526.9
D-sorbitol (glucitol) catabolism SOT lo Sorbitol (glucitol):H+ co-transporter, SOT2 (Km for sorbitol of 0.81 mM) of 491 aas and 12 TMSs (Gao et al. 2003). SOT2 of Prunus cerasus is mainly expressed only early in fruit development and not in leaves (characterized) 30% 92% 185.7 The glucose uptake porter, GluP 59% 526.9
D-fructose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 32% 76% 185.3 The glucose uptake porter, GluP 59% 526.9
sucrose catabolism Slc2a5 lo sugar transport protein 13 (characterized) 32% 76% 185.3 The glucose uptake porter, GluP 59% 526.9
glycerol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 84% 183.7 The glucose uptake porter, GluP 59% 526.9
D-mannitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 84% 183.7 The glucose uptake porter, GluP 59% 526.9
D-ribose catabolism PLT5 lo polyol transporter 5 (characterized) 31% 84% 183.7 The glucose uptake porter, GluP 59% 526.9
xylitol catabolism PLT5 lo polyol transporter 5 (characterized) 31% 84% 183.7 The glucose uptake porter, GluP 59% 526.9

Sequence Analysis Tools

View N515DRAFT_0382 at FitnessBrowser

PaperBLAST (search for papers about homologs of this protein)

Search CDD (the Conserved Domains Database, which includes COG and superfam)

Search PFam (including for weak hits, up to E = 1)

Predict protein localization: PSORTb (Gram negative bacteria)

Predict transmembrane helices and signal peptides: Phobius

Check the SEED with FIGfam search

Fitness BLAST: loading...

Sequence

MNAVEIVEGEGRATARVVLIAAAAALGGFLFGFDTAVINGAVDAVRGSFGLGAGRIGFAV
SCALLGSALGAWYAGPLADRWGRVRTMQVAAVLLAISALGSGLVAGVWDLVLWRLVGGIG
VGVASVIAPTYIAEVSPARVRGRLGSLQQLAIVLGIFAALLSDAWLAGTAGGASQKLWLG
LEAWRWMFLVAVVPALIYGSLVLGVPESPRHLVAKGRMDEAKQVLRQVLDLQDEHALQHK
LGDIAQSLRSEYRPGLRDLRGSMAGLLPVVWVGILLSVFQQFVGINVIFYYSSTLWHSVG
FSESDAFSISVVTSVVNVLVTLVAIALVDRIGRKPLLAIGSAGMTVTLGLMAWCFSQAAG
SGAALSLPAPWGMVALVAANAYVVFFGLSWGPMVWVLLGEMFPNRIRAIALAVAAAAQWV
ANFIITSSFPALSELGLSFAYGVYAFFALVSLVFVVKAVRETKGMELEEMGR

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory